Big Differences In Duplicated DNA Distinguish Chimp And Human Genomes

Dr. EvanEichler, associate professor of genome sciences at the University ofWashington in Seattle, led this study, in addition to being involved inthe Chimpanzee Genome Sequencing Project. Eichler, a Howard HughesMedical Institute investigator, and his colleagues studied the chimpgenome, looking for large-scale segmental duplications that consist ofas many as 20,000 base pairs. They found that most of the change to theoverall genome landscape between chimps and humans can be attributed tolarge segmental duplications. Such large-scale genetic events havealtered more total base pairs -- about 2.7 percent of the genome --than differences from single base-pair changes, which account for about1.2 percent of the genome.

"For all the talk of the 1.2 percentsingle base-pair difference and the importance of those, there's evenmore difference between the species due to duplication events," saidEichler. "Now we need to learn the role of those duplication events inspecies evolution and disease."

The researchers divided theduplications into three groups: those found in the chimp but not thehuman, those found in the human but not the chimp, and those found inboth species. Among the human-only duplications, some of those sectionsof the genome are implicated in human developmental disorders such asspinal muscular atrophy and Prader-Willi syndrome. Parts of thoseduplicated segments have only single copies in the chimp genome, and itis possible that the chimpanzee is therefore not predisposed to thesame diseases as a human.

About two-thirds of human-onlyduplications were new duplications in our species. They likely startedout as a single copy of a segment in an ancestral species of bothchimps and humans, and after the species split off from each other,that segment was duplicated many times in the human genome overmillions of years. Most of the remaining one-third of duplicationdifferences are due to deletion of segments in one of the two species-- the segment is deleted from the genome, copy by copy, over time.

Theresearchers found that many of the species-specific duplications havealso caused differences in gene expression. Of the individual geneswithin the duplicated segments of the genome, many of those that arespecific to either chimps or humans are expressed differently in thetwo species. Gene expression is the process through which geneticinformation is changed into structures and functions in a living cell.

Inaddition to other differences, researchers found that among sharedsegmental duplications, humans often had fewer copies of those segmentsthan chimps. The most dramatic example involved a piece of DNA near thesite of an ancient chromosome fusion point on chromosome 2. In humans,this piece of DNA is represented as four copies, but in the chimp ithas expanded to about 500 copies near the end of the chromosomes.Researchers don't yet understand why this particular piece of DNA hasbeen independently unstable in the evolution of both the human andchimp genomes.

This genome analysis project was funded by theNational Human Genome Research Institute and the National Institute ofGeneral Medical Sciences, which are both part of the NationalInstitutes of Health. It included some of Eichler's colleagues at theUW, as well researchers from the University of Bari, in Italy; the MaxPlanck Institute for Evolutionary Anthropology, in Leipzig, Germany;the Washington University School of Medicine, in St. Louis; the BACPACResource Center at Children's Hospital of Oakland Research Institute,in Oakland, Calif.; and the National Center for BiotechnologyInformation at the National Library of Medicine, in Bethesda, Md.